Description Usage Arguments Details Value Examples
Modular functions for mixed model fits
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29  lFormula(formula, data = NULL, REML = TRUE,
subset, weights, na.action, offset, contrasts = NULL,
control = lmerControl(), ...)
mkLmerDevfun(fr, X, reTrms, REML = TRUE, start = NULL,
verbose = 0, control = lmerControl(), ...)
optimizeLmer(devfun,
optimizer = formals(lmerControl)$optimizer,
restart_edge = formals(lmerControl)$restart_edge,
boundary.tol = formals(lmerControl)$boundary.tol,
start = NULL, verbose = 0L,
control = list(), ...)
glFormula(formula, data = NULL, family = gaussian,
subset, weights, na.action, offset, contrasts = NULL,
start, mustart, etastart, control = glmerControl(), ...)
mkGlmerDevfun(fr, X, reTrms, family, nAGQ = 1L,
verbose = 0L, maxit = 100L, control = glmerControl(), ...)
optimizeGlmer(devfun,
optimizer = if(stage == 1) "bobyqa" else "Nelder_Mead",
restart_edge = FALSE,
boundary.tol = formals(glmerControl)$boundary.tol,
verbose = 0L, control = list(),
nAGQ = 1L, stage = 1, start = NULL, ...)
updateGlmerDevfun(devfun, reTrms, nAGQ = 1L)

formula 
a twosided linear formula object
describing both the fixedeffects and randomeffects parts
of the model, with the response on the left of a 
data 
an optional data frame containing the
variables named in 
REML 
(logical) indicating to fit restricted maximum likelihood model. 
subset 
an optional expression indicating the
subset of the rows of 
weights 
an optional vector of ‘prior weights’ to be used
in the fitting process. Should be 
na.action 
a function that indicates what should
happen when the data contain 
offset 
this can be used to specify an a priori known
component to be included in the linear predictor during
fitting. This should be 
contrasts 
an optional 
control 
a list giving

fr 
A model frame containing the variables needed to create an

X 
fixedeffects design matrix 
reTrms 
information on random effects structure (see

start 
starting values (see 
verbose 
print output? 
maxit 
maximal number of Pwrss update iterations. 
devfun 
a deviance function, as generated by 
nAGQ 
number of GaussHermite quadrature points 
stage 
optimization stage (1: nAGQ=0, optimize over theta only; 2: nAGQ possibly >0, optimize over theta and beta) 
optimizer 
character  name of optimizing
function(s). A character vector or list of functions:
length 1 for
Special provisions are made for For 
restart_edge 
see 
boundary.tol 
see 
family 
a GLM family; see 
mustart 
optional starting values on the scale of
the conditional mean; see 
etastart 
optional starting values on the scale of
the unbounded predictor; see 
... 
other potential arguments; for 
These functions make up the internal components of an [gn]lmer fit.
[g]lFormula
takes the arguments that would normally be
passed to [g]lmer
, checking for errors and processing the
formula and data input to create a list of objects required to fit a
mixed model.
mk(GlL)merDevfun
takes the output of the previous
step (minus the formula
component) and creates a
deviance function
optimize(GlL)mer
takes a
deviance function and optimizes over theta
(or
over theta
and beta
, if stage
is set
to 2 for optimizeGlmer
updateGlmerDevfun
takes the first stage of a GLMM
optimization (with nAGQ=0
, optimizing over theta
only)
and produces a secondstage deviance function
mkMerMod
takes the environment of a
deviance function, the results of an optimization, a list of
randomeffect terms, a model frame, and a model all and produces a
[g]lmerMod
object.
lFormula
and glFormula
return a list containing
components:
model frame
fixedeffect design matrix
list containing information on random effects structure:
result of mkReTrms
(lFormula only): logical indicating if restricted maximum likelihood was used (Copy of argument.)
mkLmerDevfun
and mkGlmerDevfun
return a function to
calculate deviance (or restricted deviance) as a function of the
theta (randomeffect) parameters. updateGlmerDevfun
returns a function to calculate the deviance as a function of a
concatenation of theta and beta (fixedeffect) parameters. These
deviance functions have an environment containing objects required
for their evaluation. CAUTION: The environment
of
functions returned by mk(GlL)merDevfun
contains reference
class objects (see ReferenceClasses
,
merPredDclass
, lmRespclass
), which
behave in ways that may surprise many users. For example, if the
output of mk(GlL)merDevfun
is naively copied, then
modifications to the original will also appear in the copy (and
vice versa). To avoid this behavior one must make a deep copy (see
ReferenceClasses
for details).
optimizeLmer
and optimizeGlmer
return the results of an
optimization.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45  ### Fitting a linear mixed model in 4 modularized steps
## 1. Parse the data and formula:
lmod < lFormula(Reaction ~ Days + (DaysSubject), sleepstudy)
names(lmod)
## 2. Create the deviance function to be optimized:
(devfun < do.call(mkLmerDevfun, lmod))
ls(environment(devfun)) # the environment of 'devfun' contains objects
# required for its evaluation
## 3. Optimize the deviance function:
opt < optimizeLmer(devfun)
opt[1:3]
## 4. Package up the results:
mkMerMod(environment(devfun), opt, lmod$reTrms, fr = lmod$fr)
### Same model in one line
lmer(Reaction ~ Days + (DaysSubject), sleepstudy)
### Fitting a generalized linear mixed model in six modularized steps
## 1. Parse the data and formula:
glmod < glFormula(cbind(incidence, size  incidence) ~ period + (1  herd),
data = cbpp, family = binomial)
#.... see what've got :
str(glmod, max=1, give.attr=FALSE)
## 2. Create the deviance function for optimizing over theta:
(devfun < do.call(mkGlmerDevfun, glmod))
ls(environment(devfun)) # the environment of devfun contains lots of info
## 3. Optimize over theta using a rough approximation (i.e. nAGQ = 0):
(opt < optimizeGlmer(devfun))
## 4. Update the deviance function for optimizing over theta and beta:
(devfun < updateGlmerDevfun(devfun, glmod$reTrms))
## 5. Optimize over theta and beta:
opt < optimizeGlmer(devfun, stage=2)
str(opt, max=1) # seeing what we'got
## 6. Package up the results:
(fMod < mkMerMod(environment(devfun), opt, glmod$reTrms, fr = glmod$fr))
### Same model in one line
fM < glmer(cbind(incidence, size  incidence) ~ period + (1  herd),
data = cbpp, family = binomial)
all.equal(fMod, fM, check.attributes=FALSE, tolerance = 1e12)
#   even tolerance = 0 may work

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